Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 03:40:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d83_7453/04_2023/6d83_7453_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d83_7453/04_2023/6d83_7453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d83_7453/04_2023/6d83_7453.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d83_7453/04_2023/6d83_7453.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d83_7453/04_2023/6d83_7453_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d83_7453/04_2023/6d83_7453_updated.pdb" } resolution = 4.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 99 5.16 5 C 10538 2.51 5 N 2821 2.21 5 O 3122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "T ARG 10": "NH1" <-> "NH2" Residue "B ARG 114": "NH1" <-> "NH2" Residue "B TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "C ARG 109": "NH1" <-> "NH2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "G ARG 35": "NH1" <-> "NH2" Residue "G ARG 345": "NH1" <-> "NH2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H ARG 109": "NH1" <-> "NH2" Residue "H ARG 149": "NH1" <-> "NH2" Residue "M ARG 243": "NH1" <-> "NH2" Residue "M TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 33": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 16588 Number of models: 1 Model: "" Number of chains: 10 Chain: "T" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 1, 'TRANS': 11} Chain: "L" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 70 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "B" Number of atoms: 4513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4513 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 25, 'TRANS': 544} Chain: "C" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1330 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 3, 'TRANS': 161} Chain: "G" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4633 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 13, 'TRANS': 571} Chain: "H" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 3, 'TRANS': 159} Chain: "M" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3362 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 20, 'TRANS': 394} Chain breaks: 1 Chain: "S" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1197 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 1, 'TRANS': 140} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.43, per 1000 atoms: 0.51 Number of scatterers: 16588 At special positions: 0 Unit cell: (164.318, 133.375, 126.973, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 99 16.00 P 6 15.00 Mg 2 11.99 O 3122 8.00 N 2821 7.00 C 10538 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.46 Conformation dependent library (CDL) restraints added in 2.4 seconds 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3954 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 11 sheets defined 48.1% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'B' and resid 15 through 22 Processing helix chain 'B' and resid 27 through 43 removed outlier: 4.224A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.564A pdb=" N PHE B 51 " --> pdb=" O SER B 48 " (cutoff:3.500A) Proline residue: B 52 - end of helix No H-bonds generated for 'chain 'B' and resid 48 through 54' Processing helix chain 'B' and resid 66 through 75 Processing helix chain 'B' and resid 84 through 94 removed outlier: 3.769A pdb=" N ALA B 87 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 88 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ASN B 89 " --> pdb=" O MET B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 112 removed outlier: 4.022A pdb=" N CYS B 112 " --> pdb=" O ARG B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 130 Processing helix chain 'B' and resid 135 through 151 removed outlier: 3.555A pdb=" N VAL B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 161 through 169 removed outlier: 3.743A pdb=" N ILE B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 190 Processing helix chain 'B' and resid 201 through 209 Processing helix chain 'B' and resid 218 through 221 No H-bonds generated for 'chain 'B' and resid 218 through 221' Processing helix chain 'B' and resid 235 through 249 removed outlier: 3.934A pdb=" N ARG B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Proline residue: B 246 - end of helix removed outlier: 4.725A pdb=" N SER B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 268 removed outlier: 4.587A pdb=" N GLU B 268 " --> pdb=" O MET B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 293 removed outlier: 4.022A pdb=" N ALA B 285 " --> pdb=" O LEU B 281 " (cutoff:3.500A) Proline residue: B 286 - end of helix removed outlier: 4.479A pdb=" N LEU B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 312 removed outlier: 3.606A pdb=" N TYR B 300 " --> pdb=" O PRO B 296 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N VAL B 301 " --> pdb=" O GLU B 297 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN B 311 " --> pdb=" O ASN B 307 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LYS B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 332 through 345 removed outlier: 4.276A pdb=" N GLU B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 359 Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 388 through 401 removed outlier: 3.950A pdb=" N THR B 401 " --> pdb=" O ASP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 420 removed outlier: 4.415A pdb=" N VAL B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 432 No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 442 through 454 removed outlier: 3.773A pdb=" N ALA B 446 " --> pdb=" O PRO B 442 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ALA B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 466 Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 479 through 494 removed outlier: 3.691A pdb=" N VAL B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 511 removed outlier: 3.785A pdb=" N GLN B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 533 Processing helix chain 'B' and resid 536 through 540 Processing helix chain 'B' and resid 557 through 565 removed outlier: 3.868A pdb=" N CYS B 565 " --> pdb=" O ASP B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 572 No H-bonds generated for 'chain 'B' and resid 570 through 572' Processing helix chain 'C' and resid 30 through 38 Processing helix chain 'C' and resid 75 through 82 removed outlier: 3.673A pdb=" N TRP C 78 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG C 79 " --> pdb=" O PRO C 76 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N HIS C 80 " --> pdb=" O LEU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 110 removed outlier: 4.296A pdb=" N ASN C 101 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU C 102 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 166 through 177 Processing helix chain 'G' and resid 7 through 15 Processing helix chain 'G' and resid 20 through 38 removed outlier: 4.659A pdb=" N GLU G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU G 30 " --> pdb=" O MET G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 59 removed outlier: 3.686A pdb=" N LEU G 59 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 74 Processing helix chain 'G' and resid 79 through 92 Processing helix chain 'G' and resid 95 through 97 No H-bonds generated for 'chain 'G' and resid 95 through 97' Processing helix chain 'G' and resid 100 through 112 removed outlier: 4.370A pdb=" N ASN G 105 " --> pdb=" O LEU G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 129 removed outlier: 4.002A pdb=" N LEU G 126 " --> pdb=" O ALA G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 142 removed outlier: 3.670A pdb=" N ARG G 136 " --> pdb=" O SER G 132 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP G 137 " --> pdb=" O GLU G 133 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N GLY G 140 " --> pdb=" O ARG G 136 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLU G 141 " --> pdb=" O ASP G 137 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 146 No H-bonds generated for 'chain 'G' and resid 144 through 146' Processing helix chain 'G' and resid 151 through 167 removed outlier: 3.944A pdb=" N LYS G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS G 156 " --> pdb=" O TYR G 152 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU G 159 " --> pdb=" O LYS G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 171 No H-bonds generated for 'chain 'G' and resid 169 through 171' Processing helix chain 'G' and resid 173 through 176 No H-bonds generated for 'chain 'G' and resid 173 through 176' Processing helix chain 'G' and resid 188 through 204 Processing helix chain 'G' and resid 206 through 212 removed outlier: 4.011A pdb=" N HIS G 211 " --> pdb=" O ASP G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 227 Processing helix chain 'G' and resid 243 through 255 removed outlier: 3.769A pdb=" N ARG G 248 " --> pdb=" O PHE G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 266 Processing helix chain 'G' and resid 268 through 274 Processing helix chain 'G' and resid 283 through 298 Processing helix chain 'G' and resid 303 through 316 removed outlier: 3.848A pdb=" N LEU G 308 " --> pdb=" O GLY G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 334 Processing helix chain 'G' and resid 340 through 355 removed outlier: 3.806A pdb=" N GLN G 344 " --> pdb=" O HIS G 340 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG G 345 " --> pdb=" O ASN G 341 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N HIS G 346 " --> pdb=" O ALA G 342 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG G 347 " --> pdb=" O VAL G 343 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N SER G 348 " --> pdb=" O GLN G 344 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N THR G 349 " --> pdb=" O ARG G 345 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU G 354 " --> pdb=" O ILE G 350 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS G 355 " --> pdb=" O VAL G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 371 Processing helix chain 'G' and resid 378 through 390 removed outlier: 3.596A pdb=" N MET G 382 " --> pdb=" O ILE G 378 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS G 383 " --> pdb=" O ARG G 379 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU G 384 " --> pdb=" O GLY G 380 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 410 removed outlier: 3.631A pdb=" N PHE G 405 " --> pdb=" O ALA G 401 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS G 410 " --> pdb=" O LEU G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 428 Processing helix chain 'G' and resid 437 through 447 Processing helix chain 'G' and resid 453 through 463 removed outlier: 3.962A pdb=" N ARG G 458 " --> pdb=" O TYR G 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 470 through 487 removed outlier: 4.101A pdb=" N TRP G 478 " --> pdb=" O GLN G 474 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASP G 485 " --> pdb=" O GLY G 481 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU G 486 " --> pdb=" O GLU G 482 " (cutoff:3.500A) Processing helix chain 'G' and resid 504 through 514 removed outlier: 4.030A pdb=" N LEU G 509 " --> pdb=" O VAL G 505 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 536 removed outlier: 3.788A pdb=" N SER G 534 " --> pdb=" O ILE G 530 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR G 535 " --> pdb=" O MET G 531 " (cutoff:3.500A) Processing helix chain 'G' and resid 544 through 550 Processing helix chain 'G' and resid 557 through 572 removed outlier: 3.737A pdb=" N LEU G 569 " --> pdb=" O GLU G 565 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 38 Processing helix chain 'H' and resid 75 through 81 removed outlier: 3.708A pdb=" N TRP H 78 " --> pdb=" O ARG H 75 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG H 79 " --> pdb=" O PRO H 76 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS H 80 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 110 removed outlier: 3.703A pdb=" N VAL H 100 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASN H 101 " --> pdb=" O GLU H 98 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU H 102 " --> pdb=" O ARG H 99 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N MET H 108 " --> pdb=" O GLU H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 143 Processing helix chain 'H' and resid 145 through 147 No H-bonds generated for 'chain 'H' and resid 145 through 147' Processing helix chain 'H' and resid 166 through 177 Processing helix chain 'M' and resid 27 through 41 removed outlier: 3.727A pdb=" N VAL M 30 " --> pdb=" O MET M 27 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N HIS M 32 " --> pdb=" O GLU M 29 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N MET M 34 " --> pdb=" O GLU M 31 " (cutoff:3.500A) Proline residue: M 35 - end of helix removed outlier: 3.676A pdb=" N LYS M 40 " --> pdb=" O LEU M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 94 Processing helix chain 'M' and resid 100 through 103 No H-bonds generated for 'chain 'M' and resid 100 through 103' Processing helix chain 'M' and resid 107 through 116 removed outlier: 4.056A pdb=" N TYR M 111 " --> pdb=" O PHE M 107 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLU M 112 " --> pdb=" O VAL M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 132 Processing helix chain 'M' and resid 151 through 153 No H-bonds generated for 'chain 'M' and resid 151 through 153' Processing helix chain 'M' and resid 217 through 223 Processing helix chain 'M' and resid 244 through 250 Processing helix chain 'S' and resid 25 through 41 removed outlier: 3.564A pdb=" N SER S 41 " --> pdb=" O GLN S 37 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 95 Processing helix chain 'S' and resid 100 through 105 Processing helix chain 'S' and resid 107 through 117 Processing helix chain 'S' and resid 130 through 141 Processing sheet with id= A, first strand: chain 'C' and resid 19 through 22 removed outlier: 7.143A pdb=" N ILE C 20 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N THR C 64 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N MET C 22 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N TRP C 66 " --> pdb=" O MET C 22 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 90 through 93 removed outlier: 3.667A pdb=" N PHE C 124 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN C 126 " --> pdb=" O VAL C 92 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 153 through 157 removed outlier: 6.444A pdb=" N LEU H 121 " --> pdb=" O TYR H 154 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLN H 156 " --> pdb=" O LEU H 121 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL H 123 " --> pdb=" O GLN H 156 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLY H 24 " --> pdb=" O VAL H 68 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'M' and resid 49 through 52 removed outlier: 3.627A pdb=" N SER M 71 " --> pdb=" O ARG M 56 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR M 66 " --> pdb=" O LEU M 9 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA M 5 " --> pdb=" O THR M 70 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'M' and resid 381 through 383 removed outlier: 3.890A pdb=" N MET M 265 " --> pdb=" O ILE M 198 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N MET M 200 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLU M 263 " --> pdb=" O MET M 200 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL M 202 " --> pdb=" O GLU M 261 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU M 261 " --> pdb=" O VAL M 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'M' and resid 192 through 194 removed outlier: 3.537A pdb=" N VAL M 183 " --> pdb=" O GLN M 419 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'M' and resid 395 through 398 removed outlier: 3.588A pdb=" N ARG M 211 " --> pdb=" O LYS M 396 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ILE M 253 " --> pdb=" O LEU M 212 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'M' and resid 277 through 280 Processing sheet with id= I, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= J, first strand: chain 'M' and resid 310 through 315 removed outlier: 3.510A pdb=" N ILE M 314 " --> pdb=" O ILE M 341 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 49 through 51 removed outlier: 4.288A pdb=" N PHE S 4 " --> pdb=" O ALA S 70 " (cutoff:3.500A) 674 hydrogen bonds defined for protein. 1896 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.47 Time building geometry restraints manager: 6.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5389 1.34 - 1.46: 2858 1.46 - 1.58: 8455 1.58 - 1.69: 10 1.69 - 1.81: 161 Bond restraints: 16873 Sorted by residual: bond pdb=" C THR B 245 " pdb=" N PRO B 246 " ideal model delta sigma weight residual 1.337 1.371 -0.034 1.11e-02 8.12e+03 9.54e+00 bond pdb=" C ILE H 46 " pdb=" N PRO H 47 " ideal model delta sigma weight residual 1.333 1.354 -0.020 1.01e-02 9.80e+03 4.11e+00 bond pdb=" CA GLN B 400 " pdb=" C GLN B 400 " ideal model delta sigma weight residual 1.523 1.548 -0.025 1.34e-02 5.57e+03 3.40e+00 bond pdb=" C VAL G 216 " pdb=" N PRO G 217 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.25e-02 6.40e+03 3.24e+00 bond pdb=" CA VAL M 273 " pdb=" CB VAL M 273 " ideal model delta sigma weight residual 1.542 1.563 -0.021 1.26e-02 6.30e+03 2.76e+00 ... (remaining 16868 not shown) Histogram of bond angle deviations from ideal: 98.09 - 105.29: 296 105.29 - 112.49: 8620 112.49 - 119.69: 6065 119.69 - 126.89: 7684 126.89 - 134.09: 162 Bond angle restraints: 22827 Sorted by residual: angle pdb=" N VAL B 334 " pdb=" CA VAL B 334 " pdb=" C VAL B 334 " ideal model delta sigma weight residual 112.96 106.91 6.05 1.00e+00 1.00e+00 3.66e+01 angle pdb=" N ARG G 543 " pdb=" CA ARG G 543 " pdb=" C ARG G 543 " ideal model delta sigma weight residual 114.04 106.62 7.42 1.24e+00 6.50e-01 3.58e+01 angle pdb=" C LYS H 59 " pdb=" N ASN H 60 " pdb=" CA ASN H 60 " ideal model delta sigma weight residual 121.54 130.76 -9.22 1.91e+00 2.74e-01 2.33e+01 angle pdb=" C ASN M 308 " pdb=" N ASN M 309 " pdb=" CA ASN M 309 " ideal model delta sigma weight residual 121.54 130.18 -8.64 1.91e+00 2.74e-01 2.05e+01 angle pdb=" CA GLN B 400 " pdb=" C GLN B 400 " pdb=" N THR B 401 " ideal model delta sigma weight residual 116.84 123.65 -6.81 1.71e+00 3.42e-01 1.59e+01 ... (remaining 22822 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.15: 10206 30.15 - 60.30: 119 60.30 - 90.45: 14 90.45 - 120.61: 2 120.61 - 150.76: 7 Dihedral angle restraints: 10348 sinusoidal: 4265 harmonic: 6083 Sorted by residual: dihedral pdb=" O5' GTP H1001 " pdb=" O3A GTP H1001 " pdb=" PA GTP H1001 " pdb=" PB GTP H1001 " ideal model delta sinusoidal sigma weight residual -85.88 64.88 -150.76 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" CA GLU B 295 " pdb=" C GLU B 295 " pdb=" N PRO B 296 " pdb=" CA PRO B 296 " ideal model delta harmonic sigma weight residual 180.00 -146.57 -33.43 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" O3B GTP C1001 " pdb=" O3A GTP C1001 " pdb=" PB GTP C1001 " pdb=" PA GTP C1001 " ideal model delta sinusoidal sigma weight residual 291.08 146.93 144.15 1 2.00e+01 2.50e-03 4.35e+01 ... (remaining 10345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2215 0.071 - 0.143: 390 0.143 - 0.214: 25 0.214 - 0.285: 3 0.285 - 0.356: 1 Chirality restraints: 2634 Sorted by residual: chirality pdb=" CB VAL B 47 " pdb=" CA VAL B 47 " pdb=" CG1 VAL B 47 " pdb=" CG2 VAL B 47 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CG LEU B 197 " pdb=" CB LEU B 197 " pdb=" CD1 LEU B 197 " pdb=" CD2 LEU B 197 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA ASN H 60 " pdb=" N ASN H 60 " pdb=" C ASN H 60 " pdb=" CB ASN H 60 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2631 not shown) Planarity restraints: 2890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO M 374 " 0.047 5.00e-02 4.00e+02 7.13e-02 8.14e+00 pdb=" N PRO M 375 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO M 375 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO M 375 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 75 " 0.038 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO H 76 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO H 76 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 76 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 97 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO B 98 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 98 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 98 " 0.031 5.00e-02 4.00e+02 ... (remaining 2887 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 91 2.50 - 3.10: 11378 3.10 - 3.70: 25528 3.70 - 4.30: 36448 4.30 - 4.90: 59111 Nonbonded interactions: 132556 Sorted by model distance: nonbonded pdb=" O2G GTP C1001 " pdb="MG MG C1002 " model vdw 1.904 2.170 nonbonded pdb=" O2G GTP H1001 " pdb="MG MG H1002 " model vdw 1.907 2.170 nonbonded pdb=" O1G GTP H1001 " pdb="MG MG H1002 " model vdw 1.954 2.170 nonbonded pdb=" CG2 THR H 31 " pdb="MG MG H1002 " model vdw 2.113 2.590 nonbonded pdb=" PG GTP H1001 " pdb="MG MG H1002 " model vdw 2.192 2.530 ... (remaining 132551 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 17 through 179 or resid 1001 through 1002)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.190 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 40.250 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 16873 Z= 0.318 Angle : 0.922 9.855 22827 Z= 0.525 Chirality : 0.053 0.356 2634 Planarity : 0.006 0.071 2890 Dihedral : 11.341 150.758 6394 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.04 % Favored : 94.91 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.30 (0.15), residues: 2045 helix: -2.79 (0.11), residues: 1039 sheet: -3.08 (0.30), residues: 246 loop : -2.53 (0.19), residues: 760 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 724 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 725 average time/residue: 0.3439 time to fit residues: 350.0334 Evaluate side-chains 332 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 1.851 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 chunk 85 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 159 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 185 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 ASN B 173 ASN B 205 ASN B 319 HIS ** B 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN B 483 GLN B 505 GLN B 575 HIS C 128 GLN C 150 HIS ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 GLN G 235 HIS ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 443 GLN G 447 ASN G 452 HIS ** G 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 GLN H 128 GLN H 150 HIS H 156 GLN H 176 GLN M 239 HIS M 240 GLN M 270 ASN M 300 GLN S 3 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.081 16873 Z= 0.206 Angle : 0.666 14.847 22827 Z= 0.337 Chirality : 0.045 0.202 2634 Planarity : 0.006 0.190 2890 Dihedral : 10.194 141.902 2272 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.17), residues: 2045 helix: -1.33 (0.14), residues: 1035 sheet: -2.77 (0.29), residues: 259 loop : -2.00 (0.21), residues: 751 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 477 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 478 average time/residue: 0.3255 time to fit residues: 224.3055 Evaluate side-chains 274 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 2.133 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 154 optimal weight: 0.8980 chunk 126 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 185 optimal weight: 0.9980 chunk 200 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** G 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 323 ASN ** G 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS ** M 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 239 HIS M 270 ASN ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 16873 Z= 0.233 Angle : 0.648 13.960 22827 Z= 0.327 Chirality : 0.044 0.166 2634 Planarity : 0.005 0.146 2890 Dihedral : 10.005 138.411 2272 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.18), residues: 2045 helix: -0.63 (0.15), residues: 1038 sheet: -2.52 (0.30), residues: 260 loop : -1.77 (0.22), residues: 747 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 417 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 417 average time/residue: 0.2875 time to fit residues: 180.9409 Evaluate side-chains 268 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 2.062 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 8.9990 chunk 139 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 124 optimal weight: 0.0050 chunk 186 optimal weight: 6.9990 chunk 197 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 176 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 89 ASN B 173 ASN ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 ASN C 128 GLN G 97 GLN ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 470 GLN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.092 16873 Z= 0.210 Angle : 0.634 13.618 22827 Z= 0.319 Chirality : 0.044 0.203 2634 Planarity : 0.005 0.134 2890 Dihedral : 9.917 138.684 2272 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.18), residues: 2045 helix: -0.34 (0.16), residues: 1045 sheet: -2.22 (0.31), residues: 262 loop : -1.64 (0.22), residues: 738 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 406 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 407 average time/residue: 0.2721 time to fit residues: 168.9743 Evaluate side-chains 265 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 264 time to evaluate : 2.251 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1883 time to fit residues: 3.0916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 146 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 176 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN B 205 ASN B 319 HIS ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 408 GLN ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 ASN C 128 GLN G 97 GLN ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 308 ASN ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 16873 Z= 0.179 Angle : 0.610 13.695 22827 Z= 0.301 Chirality : 0.043 0.201 2634 Planarity : 0.004 0.095 2890 Dihedral : 9.721 138.487 2272 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.19), residues: 2045 helix: -0.14 (0.16), residues: 1061 sheet: -2.11 (0.32), residues: 253 loop : -1.49 (0.23), residues: 731 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 411 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 412 average time/residue: 0.2969 time to fit residues: 186.8574 Evaluate side-chains 282 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 2.169 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 115 optimal weight: 0.0070 chunk 48 optimal weight: 8.9990 chunk 197 optimal weight: 8.9990 chunk 163 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 ASN B 319 HIS ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN G 28 GLN G 97 GLN ** G 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS M 249 ASN M 288 HIS ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 16873 Z= 0.227 Angle : 0.644 14.822 22827 Z= 0.320 Chirality : 0.045 0.219 2634 Planarity : 0.005 0.119 2890 Dihedral : 9.683 137.792 2272 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.19), residues: 2045 helix: 0.00 (0.16), residues: 1059 sheet: -2.00 (0.32), residues: 257 loop : -1.33 (0.23), residues: 729 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 2.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 385 average time/residue: 0.2903 time to fit residues: 168.5902 Evaluate side-chains 265 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 2.193 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 112 optimal weight: 0.0270 chunk 144 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 196 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 119 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 HIS ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN G 97 GLN ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 249 ASN ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 16873 Z= 0.172 Angle : 0.629 14.584 22827 Z= 0.308 Chirality : 0.044 0.190 2634 Planarity : 0.004 0.100 2890 Dihedral : 9.535 138.377 2272 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.19), residues: 2045 helix: 0.10 (0.16), residues: 1060 sheet: -1.90 (0.32), residues: 259 loop : -1.25 (0.23), residues: 726 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 403 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 0.2910 time to fit residues: 180.5797 Evaluate side-chains 275 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 2.031 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 0.0170 chunk 59 optimal weight: 0.9980 chunk 38 optimal weight: 0.0070 chunk 125 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 18 optimal weight: 0.0870 chunk 154 optimal weight: 3.9990 chunk 178 optimal weight: 9.9990 overall best weight: 0.3614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 HIS B 386 GLN ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS C 128 GLN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 16873 Z= 0.164 Angle : 0.651 14.741 22827 Z= 0.316 Chirality : 0.044 0.354 2634 Planarity : 0.005 0.095 2890 Dihedral : 9.452 141.758 2272 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.19), residues: 2045 helix: 0.14 (0.16), residues: 1063 sheet: -1.67 (0.33), residues: 250 loop : -1.19 (0.23), residues: 732 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.2831 time to fit residues: 170.7979 Evaluate side-chains 275 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 1.823 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 173 optimal weight: 0.2980 chunk 182 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 HIS ** B 435 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 16873 Z= 0.188 Angle : 0.666 14.683 22827 Z= 0.323 Chirality : 0.045 0.341 2634 Planarity : 0.004 0.082 2890 Dihedral : 9.352 145.711 2272 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.19), residues: 2045 helix: 0.12 (0.16), residues: 1059 sheet: -1.65 (0.32), residues: 253 loop : -1.07 (0.24), residues: 733 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 386 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 386 average time/residue: 0.2726 time to fit residues: 162.2371 Evaluate side-chains 276 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 2.077 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 134 optimal weight: 6.9990 chunk 203 optimal weight: 0.9980 chunk 187 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 16 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 128 optimal weight: 0.0060 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 319 HIS ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS C 128 GLN G 311 ASN ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.5790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 16873 Z= 0.238 Angle : 0.681 14.736 22827 Z= 0.336 Chirality : 0.046 0.356 2634 Planarity : 0.004 0.054 2890 Dihedral : 9.332 149.478 2272 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.19), residues: 2045 helix: 0.21 (0.16), residues: 1054 sheet: -1.60 (0.33), residues: 252 loop : -1.05 (0.24), residues: 739 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4090 Ramachandran restraints generated. 2045 Oldfield, 0 Emsley, 2045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 1.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 371 average time/residue: 0.2660 time to fit residues: 153.6561 Evaluate side-chains 268 residues out of total 1842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 2.022 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 23 optimal weight: 0.1980 chunk 44 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 67 optimal weight: 0.0770 chunk 166 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 29 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 overall best weight: 0.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 HIS B 435 ASN ** B 481 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS C 128 GLN ** G 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 418 HIS ** H 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.094692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.082078 restraints weight = 54923.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.083812 restraints weight = 34902.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.085057 restraints weight = 24539.674| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.5892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 16873 Z= 0.188 Angle : 0.683 14.735 22827 Z= 0.329 Chirality : 0.045 0.285 2634 Planarity : 0.004 0.049 2890 Dihedral : 9.195 155.040 2272 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.19), residues: 2045 helix: 0.21 (0.16), residues: 1057 sheet: -1.64 (0.32), residues: 252 loop : -1.05 (0.24), residues: 736 =============================================================================== Job complete usr+sys time: 3890.23 seconds wall clock time: 71 minutes 17.09 seconds (4277.09 seconds total)